The Final Five visit the temple while retracing their tribe's trip from Kobol. As a result of sub-light travel, this visit takes place some number of years after the fall of the 13th colony and the similarly dated fall of Kobol. Ellen Tigh describes it not as a temple of five priests, but as a temple built to pray for guidance on the trip to Earth. John Cavil says that its new moniker is a testament to the Final Five's vanity. Tigh tells Cavil that they did not modify the temple to show their faces. She suggests that this modification is the work of the "one true god." (No Exit).

The temple is rediscovered by Galen Tyrol months after the fleet's exodus from New Caprica. Tyrol mysteriously senses the Temple's presence in a nearby mountain side. As he is one of the Final Five, his buried memories likely unconsciously guided him there.

The Cylons are interested in the location as well, guided by a Hybrid's cryptic information on the location of the Eye of Jupiter, an artifact that supposedly points the way to Earth. One Cylon, a Number Three, believes a correlation exists between the Temple and the five missing Cylons lost to memory. The Colonials note that the Temple is related to five priests in some way, but Roslin's full detailing of this connection to Admiral Adama is interrupted by another crisis.

The Eye's location, its form or purpose is sought by the Colonials and Cylons. Chief Tyrol studies the circular decorations, or mandalas, as well as ancient glyphs located on the central spire.

In fear of the Cylons capturing the site, the Colonials place multiple G-4 packs around the central spire for use in the event of the Temple's imminent compromise (The Eye of Jupiter).

After the algae planet's star begins to nova, Tyrol and other Colonials, watching the event after evacuating the Temple, realize that the dying star's appearance greatly resembles the Temple's mandala, indicating that the Eye of Jupiter is actually the star itself. The Colonials attempt to destroy the Temple, but a Cylon party has entered the structure moments earlier and removes the detonation caps from the explosives.

The star's light or another effect soon activates the mechanisms inside the Temple. The Number Three enters a shaft of light hitting one spot within the Temple, where she witnesses a persistent image of the missing five Cylons. However, when the device deactivates, she dies on the spot. Gaius Baltar attempts to use the now inactive vision system after Three's death, but is captured by Chief Tyrol and eventually returned to Galactica.

As with much in the star system, the Temple of Five is destroyed as the nova's shockwave obliterates the planet. A review of the event by the Fleet's leadership determines that the Thirteenth Tribe used the Temple of Five (and its star) as a visual reference to the next way point to Earth, the nebular remains of a similar nova in the Ionian system (Rapture).

Galen Tyrol's discovery of the Temple of Five may be related to being one of the Final Five; themselves having come from the home of the Thirteenth Tribe, according to the Hybrid in "Faith". The Five apparently visited it on their way to the Colonies so its location was in Tyrol's blocked Cylon memories. Those blocked memories may have subsconciously guided him there.